Nanopore sequencing

On the left is a drawing of the complex formed between alpha-hemolysin and dsDNA with linkage through an oligomer. On the right, movement of this complex in relation to a nanopore channel is shown sequentially in two steps (I) and (II). Once the complex is inserted into the nanopore, the alpha-hemolysin protein will be functional in the newly formed hybrid, biological and solid state, nanopore system.
Illustration of how an electrical signal is generated from DNA passing through a nanopore channel.

Nanopore sequencing is a third generation[1] approach used in the sequencing of biopolymers — specifically, polynucleotides in the form of DNA or RNA.

Using nanopore sequencing, a single molecule of DNA or RNA can be sequenced without the need for PCR amplification or chemical labeling of the sample. Nanopore sequencing has the potential to offer relatively low-cost genotyping, high mobility for testing, and rapid processing of samples with the ability to display results in real-time. Publications on the method outline its use in rapid identification of viral pathogens,[2][3][4] monitoring ebola,[5] environmental monitoring,[6] food safety monitoring, human genome sequencing,[7] plant genome sequencing,[8] monitoring of antibiotic resistance,[9] haplotyping[10] and other applications.

  1. ^ Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE (June 2011). "Landscape of next-generation sequencing technologies". Analytical Chemistry. 83 (12): 4327–41. doi:10.1021/ac2010857. PMC 3437308. PMID 21612267.
  2. ^ Greninger AL, Naccache SN, Federman S, Yu G, Mbala P, Bres V, et al. (September 2015). "Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis". Genome Medicine. 7 (1): 99. bioRxiv 10.1101/020420. doi:10.1186/s13073-015-0220-9. PMC 4587849. PMID 26416663.
  3. ^ Biclot, Anaïs (2023-05-29). "Technology to tackle viral infections". Retrieved 2023-07-07.
  4. ^ Munro, Rory; Holmes, Nadine; Moore, Christopher; Carlile, Matthew; Payne, Alexander; Tyson, John R.; Williams, Thomas; Alder, Christopher; Snell, Luke B.; Nebbia, Gaia; Santos, Roberto; Loose, Matt (2023). "A framework for real-time monitoring, analysis and adaptive sampling of viral amplicon nanopore sequencing". Frontiers in Genetics. 14. doi:10.3389/fgene.2023.1138582. ISSN 1664-8021. PMC 10083257. PMID 37051600.
  5. ^ Nick Loman (15 May 2015). "How a small backpack for fast genomic sequencing is helping combat Ebola". The Conversation.
  6. ^ "TGAC's take on the first portable DNA sequencing 'laboratory'". EurekAlert!. 19 March 2015.
  7. ^ "nanopore-wgs-consortium/NA12878". GitHub. Retrieved 2017-01-10.
  8. ^ "Solanum pennellii (new cultivar) - PlabiPD". www.plabipd.de. Retrieved 2017-01-10.
  9. ^ Cao MD, Ganesamoorthy D, Elliott AG, Zhang H, Cooper MA, Coin LJ (July 2016). "Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION(TM) sequencing". GigaScience. 5 (1): 32. bioRxiv 10.1101/019356. doi:10.1186/s13742-016-0137-2. PMC 4960868. PMID 27457073.
  10. ^ Ammar R, Paton TA, Torti D, Shlien A, Bader GD (2015). "CYP2D6 variants and haplotypes". F1000Research. 4: 17. doi:10.12688/f1000research.6037.2. PMC 4392832. PMID 25901276.